Increasing the Productivity of Glycopeptides Analysis by Using Higher-Energy Collision Dissociation-Accurate Mass-Product-Dependent Electron Transfer Dissociation

Currently, glycans are attracting attention from the scientific community as potential biomarkers or as posttranslational modifications (PTMs) of therapeutic proteins. However, structural characterization of glycoproteins and glycopeptides remains analytically challenging. Here, we report on the implementation of a novel acquisition strategy termed higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation (HCD-PD-ETD) on a hybrid linear ion trap-orbitrap mass spectrometer. This acquisition strategy uses the complementary fragmentations of ETD and HCD for glycopeptides analysis in an intelligent fashion. Furthermore, the approach minimizes user input for optimizing instrumental parameters and enables straightforward detection of glycopeptides. ETD spectra are only acquired when glycan oxonium ions from MS/MS HCD are detected. The advantage of this approach is that it streamlines data analysis and improves dynamic range and duty cycle. Here, we present the benefits of HCD-PD-ETD relative to the traditional alternating HCD/ETD for a trainer set containing twelve-protein mixture with two glycoproteins: human serotransferrin, ovalbumin and contaminations of two other: bovine alpha 1 acid glycoprotein (bAGP) and bovine fetuin

In vivo aging of rat skeletal muscle sarcoplasmic reticulum Ca-ATPase. Chemical analysis and quantitative simulation by exposure to low levels of peroxyl radicals

AbstractSarcoplasmic reticulum (SR) Ca-ATPase of young adult (5 months) and aged (28 months) Fischer 344 male rat skeletal muscle was analyzed for posttranslational modifications as a result of biological aging and their potential functional consequences. The significant differences in the amino acid composition were a 6.8% lower content of sulfhydryl groups and a ca. 4% lower content of Arg residues of the Ca-ATPase from old as compared to young rats. Based on a total of 24 Cys residues the difference in protein thiols corresponds to a loss of 1.5 mol Cys/mol Ca-ATPase as a result of in vivo aging. The loss of Cys residues was not accompanied by a loss of enzyme activity though the `aged' Ca-ATPase was more sensitive to heat inactivation, aggregation, and tryptic digestion. A comparison of the total sulfhydryl content of all SR proteins present revealed a 13% lower amount for SR vesicles isolated from aged rats. Compared to the alterations of Cys and Arg, there was only a slight and probably physiologically insignificant increase of protein carbonyls with aging, i.e. from 0.32 to 0.46 mol carbonyl groups per mol of Ca-ATPase. When SR vesicles from young rats were exposed to AAPH-derived peroxyl radicals, there was a loss of ca. 1.38×10−4 M total SR sulfhydryl groups per 4 mg SR protein/ml (corresponding to ca. 25%) and a loss of 9.6×10−5 M Ca-ATPase sulfhydryl groups (corresponding to ca. 31%) per 1.6×10−5 M initiating peroxyl radicals, indicating that the stoichiometry of sulfhydryl oxidation was ≥6 oxidized thiols per initiating AAPH-derived peroxyl radical. Besides Cys, the exposure to AAPH-derived radicals caused a slight loss of Ca-ATPase Arg, Met, and Ser residues. Most importantly, the SR Ca-ATPase exposed to this low concentration of peroxyl radicals displayed physical and functional properties quantitatively comparable to those of SR Ca-ATPase isolated from aged rats, i.e. no immediate loss of activity, increased susceptibility to heat inactivation, aggregation, and tryptic digestion. Moreover, a comparison of kinetically early tryptic fragments by HPLC-electrospray MS and N-terminal sequencing revealed that similar peptide fragments were produced from `aged' and AAPH-oxidized Ca-ATPase which were not (or kinetically significantly later) generated from the `young' Ca-ATPase, suggesting some conformational changes of the Ca-ATPase as a result of aging and AAPH-exposure. All except one of these peptides originated from locations remote from the nucleotide-binding and calcium-binding sites. The latter results suggest that aging and AAPH-exposure may target similar Cys residues, mainly at locations remote from the nucleotide-binding and calcium-binding sites, rationalizing the fact that Cys oxidation did not immediately cause inactivation of the Ca-ATPase. Our results provide a quantitative estimate of a net concentration of reactive oxygen species, here peroxyl radicals, which induces physical and chemical alterations of the SR Ca-ATPase quantitatively comparable to those induced by in vivo aging

Initiating change locally in bullying and aggression through the school environment (INCLUSIVE) trial: update to cluster randomised controlled trial protocol.

BACKGROUND: Systematic reviews suggest that multi-component interventions are effective in reducing bullying victimisation and perpetration. We are undertaking a phase III randomised trial of the INCLUSIVE multi-component intervention. This trial aims to assess the effectiveness and cost-effectiveness of the INCLUSIVE intervention in reducing aggression and bullying victimisation in English secondary schools. This paper updates the original trial protocol published in 2014 (Trials 15:381, 2014) and presents the changes in the process evaluation protocol and the secondary outcome data collection. METHODS: The methods are summarised as follows. DESIGN: cluster randomised trial. PARTICIPANTS: 40 state secondary schools. Outcomes assessed among the cohort of students at the end of year 7 (n = 6667) at baseline. INTERVENTION: INCLUSIVE is a multi-component school intervention including a social and emotional learning curriculum, changes to school environment (an action group comprising staff and students reviews local data on needs to review rules and policies and determine other local actions) and staff training in restorative practice. The intervention will be delivered by schools supported in the first two years by educational facilitators independent of the research team, with a third intervention year involving no external facilitation but all other elements. Comparator: normal practice. OUTCOMES: Primary: Two primary outcomes at student level assessed at baseline and at 36 months: 1. Aggressive behaviours in school: Edinburgh Study of Youth Transitions and Crime school misbehaviour subscale (ESYTC) 2. Bullying and victimisation: Gatehouse Bullying Scale (GBS) Secondary outcomes assessed at baseline, 24 and 36 months will include measures relating to the economic evaluation, psychosocial outcomes in students and staff and school-level truancy and exclusion rates. SAMPLE SIZE: 20 schools per arm will provide 90% power to identify an effect size of 0.25 SD with a 5% significance level. Randomisation: eligible consenting schools were randomised stratified for single-sex versus mixed-sex schools, school-level deprivation and measures of school attainment. DISCUSSION: The trial involves independent research and intervention teams and is supervised by a Trial Steering Committee and a Data Monitoring Committee. TRIAL REGISTRATION: Current Controlled Trials, ISRCTN10751359 . Registered on 11 March 2014

A draft map of the mouse pluripotent stem cell spatial proteome.

Knowledge of the subcellular distribution of proteins is vital for understanding cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning proteins to subcellular niches with low resolution and/or accuracy. Here we introduce hyperLOPIT, a method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry with multivariate data analysis. We apply hyperLOPIT to a pluripotent stem cell population whose subcellular proteome has not been extensively studied. We provide localization data on over 5,000 proteins with unprecedented spatial resolution to reveal the organization of organelles, sub-organellar compartments, protein complexes, functional networks and steady-state dynamics of proteins and unexpected subcellular locations. The method paves the way for characterizing the impact of post-transcriptional and post-translational modification on protein location and studies involving proteome-level locational changes on cellular perturbation. An interactive open-source resource is presented that enables exploration of these data.The authors thank Andreas Hühmer, Philip Remes, Jesse Canterbury and Graeme McAlister of Thermo Fisher Scientific, San Jose, CA, USA, for their advice regarding operation of the Orbitrap Fusion. We also thank Mike Deery for assistance with checking sample integrity on the mass spectrometers in the Cambridge Centre for Proteomics on equipment purchased via a Wellcome Trust grant (099135/Z/12/Z ), and Brian Hendrich of the Wellcome Trust-MRC Stem Cell Institute in Cambridge and Sean Munro of the MRC Laboratory of Molecular Biology in Cambridge for insightful comments about the data. AC was supported by BBSRC grant (BB/D526088/1). C.M.M. and L.G. were supported by European Union 7th Framework Program (PRIMEXS project, grant agreement number 262067), L.M.B was supported by a BBSRC Tools and Resources Development Fund (Award BB/K00137X/1), and P.C.H. was supported by an ERC Advanced Investigator grant to A.M.A. A.G. was funded through the Alexander S. Onassis Public Benefit Foundation, the Foundation for Education and European Culture (IPEP) and the Embiricos Trust Scholarship of Jesus College Cambridge. T.H. was supported by Commonwealth Split Site PhD Scholarship. T.N. was supported by an ERASMUS Placement scholarshipThis is the final version of the article. It was first available from NPG via http://dx.doi.org/10.1038/ncomms999

Proteome-wide analysis of Trypanosoma cruzi exponential and stationary growth phases reveals a subcellular compartment-specific regulation

Trypanosoma cruzi, the etiologic agent of Chagas disease, cycles through different life stages characterized by defined molecular traits associated with the proliferative or differentiation state. In particular, T. cruzi epimastigotes are the replicative forms that colonize the intestine of the Triatomine insect vector before entering the stationary phase that is crucial for differentiation into metacyclic trypomastigotes, which are the infective forms of mammalian hosts. The transition from proliferative exponential phase to quiescent stationary phase represents an important step that recapitulates the early molecular events of metacyclogenesis, opening new possibilities for understanding this process. In this study, we report a quantitative shotgun proteomic analysis of the T. cruzi epimastigote in the exponential and stationary growth phases. More than 3000 proteins were detected and quantified, highlighting the regulation of proteins involved in different subcellular compartments. Ribosomal proteins were upregulated in the exponential phase, supporting the higher replication rate of this growth phase. Autophagy-related proteins were upregulated in the stationary growth phase, indicating the onset of the metacyclogenesis process. Moreover, this study reports the regulation of N-terminally acetylated proteins during growth phase transitioning, adding a new layer of regulation to this process. Taken together, this study reports a proteome-wide rewiring during T. cruzi transit from the replicative exponential phase to the stationary growth phase, which is the preparatory phase for differentiation

Glycoproteomic Analysis of the Aortic Extracellular Matrix in Marfan Patients.

OBJECTIVE: Marfan syndrome (MFS) is caused by mutations in FBN1 (fibrillin-1), an extracellular matrix (ECM) component, which is modified post-translationally by glycosylation. This study aimed to characterize the glycoproteome of the aortic ECM from patients with MFS and relate it to aortopathy. Approach and Results: ECM extracts of aneurysmal ascending aortic tissue from patients with and without MFS were enriched for glycopeptides. Direct N-glycopeptide analysis by mass spectrometry identified 141 glycoforms from 47 glycosites within 35 glycoproteins in the human aortic ECM. Notably, MFAP4 (microfibril-associated glycoprotein 4) showed increased and more diverse N-glycosylation in patients with MFS compared with control patients. MFAP4 mRNA levels were markedly higher in MFS aortic tissue. MFAP4 protein levels were also increased at the predilection (convexity) site for ascending aorta aneurysm in bicuspid aortic valve patients, preceding aortic dilatation. In human aortic smooth muscle cells, MFAP4 mRNA expression was induced by TGF (transforming growth factor)-β1 whereas siRNA knockdown of MFAP4 decreased FBN1 but increased elastin expression. These ECM changes were accompanied by differential gene expression and protein abundance of proteases from ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family and their proteoglycan substrates, respectively. Finally, high plasma MFAP4 concentrations in patients with MFS were associated with a lower thoracic descending aorta distensibility and greater incidence of type B aortic dissection during 68 months follow-up. CONCLUSIONS: Our glycoproteomics analysis revealed that MFAP4 glycosylation is enhanced, as well as its expression during the advanced, aneurysmal stages of MFS compared with control aneurysms from patients without MFS

Qualitative study of the feasibility and acceptability of implementation, and potential mechanisms of Learning Together for Mental Health, a whole-school intervention aiming to promote mental health and wellbeing in secondary schools.

Despite high rates of adolescent mental-health problems, there are few effective whole-school interventions to address this. Whole-school interventions offer a feasible and sustainable means of promoting mental health. We previously evaluated the Learning Together (LT) intervention which was effective in preventing bullying (primary outcome), promoting mental well-being, psychological functioning, and reducing substance use (secondary outcomes). We adapted LT to develop Learning Together for Mental Health (LTMH) with a new menu of evidence-based actions to address mental health and an enhanced SEL curriculum. Methods: We undertook a feasibility study of LTMH, a whole-school intervention featuring needs assessment, student and staff participation in decision-making via action groups selecting actions from an evidence-based menu, restorative practice, and a SEL and resilience skills curriculum between 2022 and 2023. This article examines the feasibility, acceptability, and potential mechanisms of LTMH, qualitatively, drawing on interviews and focus groups with 49 students in years 8 and 10, and 20 staff across four state secondary schools in southern England. Results: The intervention was feasible and acceptable to implement. Ierms of feasibility, the SEL curriculum was the most challenging to implement and was not prioritised by schools that had existing social and emotional learning lessons. Training and external facilitation were well-rated. Some schools struggled with the resourcing and workload implications of implementing actions from the evidence-based menu. Some aspects were not clear. Some staff were not aware that the various components worked together. Needs reports were not easy to understand for all. Students were generally supportive of restorative practice and SEL lessons. Data supported a potential mechanism involving increased school belonging and developing practical knowledge and skills to manage emotions and relationships. The intervention has little potential for harm. Conclusions: The intervention is ready for phase III trial with minor adaptations. A phase III trial of effectiveness is justified.Trial registration ISRCTN15301591 https://doi.org/10.1186/ISRCTN15301591

Modifying the secondary school environment to reduce bullying and aggression: the INCLUSIVE cluster RCT

BackgroundBullying, aggression and violence among children and young people are some of the most consequential public mental health problems.ObjectivesThe INCLUSIVE (initiating change locally in bullying and aggression through the school environment) trial evaluated the Learning Together intervention, which involved students in efforts to modify their school environment using restorative approaches and to develop social and emotional skills. We hypothesised that in schools receiving Learning Together there would be lower rates of self-reported bullying and perpetration of aggression and improved student biopsychosocial health at follow-up than in control schools.DesignINCLUSIVE was a cluster randomised trial with integral economic and process evaluations.SettingForty secondary schools in south-east England took part. Schools were randomly assigned to implement the Learning Together intervention over 3 years or to continue standard practice (controls).ParticipantsA total of 6667 (93.6%) students participated at baseline and 5960 (83.3%) students participated at final follow-up. No schools withdrew from the study.InterventionSchools were provided with (1) a social and emotional curriculum, (2) all-staff training in restorative approaches, (3) an external facilitator to help convene an action group to revise rules and policies and to oversee intervention delivery and (4) information on local needs to inform decisions.Main outcome measuresSelf-reported experience of bullying victimisation (Gatehouse Bullying Scale) and perpetration of aggression (Edinburgh Study of Youth Transitions and Crime school misbehaviour subscale) measured at 36 months. Intention-to-treat analysis using longitudinal mixed-effects models.ResultsPrimary outcomes – Gatehouse Bullying Scale scores were significantly lower among intervention schools than among control schools at 36 months (adjusted mean difference –0.03, 95% confidence interval –0.06 to 0.00). There was no evidence of a difference in Edinburgh Study of Youth Transitions and Crime scores. Secondary outcomes – students in intervention schools had higher quality of life (adjusted mean difference 1.44, 95% confidence interval 0.07 to 2.17) and psychological well-being scores (adjusted mean difference 0.33, 95% confidence interval 0.00 to 0.66), lower psychological total difficulties (Strengths and Difficulties Questionnaire) score (adjusted mean difference –0.54, 95% confidence interval –0.83 to –0.25), and lower odds of having smoked (odds ratio 0.58, 95% confidence interval 0.43 to 0.80), drunk alcohol (odds ratio 0.72, 95% confidence interval 0.56 to 0.92), been offered or tried illicit drugs (odds ratio 0.51, 95% confidence interval 0.36 to 0.73) and been in contact with police in the previous 12 months (odds ratio 0.74, 95% confidence interval 0.56 to 0.97). The total numbers of reported serious adverse events were similar in each arm. There were no changes for staff outcomes. Process evaluation – fidelity was variable, with a reduction in year 3. Over half of the staff were aware that the school was taking steps to reduce bullying and aggression. Economic evaluation – mean (standard deviation) total education sector-related costs were £116 (£47) per pupil in the control arm compared with £163 (£69) in the intervention arm over the first two facilitated years, and £63 (£33) and £74 (£37) per pupil, respectively, in the final, unfacilitated, year. Overall, the intervention was associated with higher costs, but the mean gain in students’ health-related quality of life was slightly higher in the intervention arm. The incremental cost per quality-adjusted life year was £13,284 (95% confidence interval –£32,175 to £58,743) and £1875 (95% confidence interval –£12,945 to £16,695) at 2 and 3 years, respectively.LimitationsOur trial was carried out in urban and periurban settings in the counties around London. The large number of secondary outcomes investigated necessitated multiple statistical testing. Fidelity of implementation of Learning Together was variable.ConclusionsLearning Together is effective across a very broad range of key public health targets for adolescents.Future workFurther studies are required to assess refined versions of this intervention in other settings.Trial registrationCurrent Controlled Trials ISRCTN10751359.FundingThis project was funded by the National Institute for Health Research (NIHR) Public Health Research programme and will be published in full inPublic Health Research; Vol. 7, No. 18. See the NIHR Journals Library website for further project information. Additional funding was provided by the Educational Endowment Foundation.</jats:sec

The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile

<p>Abstract</p> <p>Background</p> <p>Overall gastric cancer survival remains poor mainly because there are no reliable methods for identifying highly curable early stage disease. Multi-protein profiling of gastric fluids, obtained from the anatomic site of pathology, could reveal diagnostic proteomic fingerprints.</p> <p>Methods</p> <p>Protein profiles were generated from gastric fluid samples of 19 gastric cancer and 36 benign gastritides patients undergoing elective, clinically-indicated gastroscopy using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry on multiple ProteinChip arrays. Proteomic features were compared by significance analysis of microarray algorithm and two-way hierarchical clustering. A second blinded sample set (24 gastric cancers and 29 clinically benign gastritides) was used for validation.</p> <p>Results</p> <p>By significance analysyis of microarray, 60 proteomic features were up-regulated and 46 were down-regulated in gastric cancer samples (<it>p </it>< 0.01). Multimarker clustering showed two distinctive proteomic profiles independent of age and ethnicity. Eighteen of 19 cancer samples clustered together (sensitivity 95%) while 27/36 of non-cancer samples clustered in a second group. Nine non-cancer samples that clustered with cancer samples included 5 pre-malignant lesions (1 adenomatous polyp and 4 intestinal metaplasia). Validation using a second sample set showed the sensitivity and specificity to be 88% and 93%, respectively. Positive predictive value of the combined data was 0.80. Selected peptide sequencing identified pepsinogen C and pepsin A activation peptide as significantly down-regulated and alpha-defensin as significantly up-regulated.</p> <p>Conclusion</p> <p>This simple and reproducible multimarker proteomic assay could supplement clinical gastroscopic evaluation of symptomatic patients to enhance diagnostic accuracy for gastric cancer and pre-malignant lesions.</p